Contacts of the helix formed by residues 494 - 501 (chain E) in PDB entry 2P1N
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 494 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470E ASP* 2.5 19.2 + - - +
473E MET* 4.1 5.1 - - - +
493E PHE* 1.3 76.6 - - - +
495E ASP* 1.3 64.4 + - - -
498E LEU* 3.4 21.1 + - - +
513E MET* 4.3 0.2 - - - +
517E SER* 3.4 24.4 - - - -
518E VAL* 3.7 9.3 - - - +
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Residues in contact with ASP 495 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495B ASP* 6.0 1.3 - - + -
496B LYS* 3.7 18.5 - - + +
470E ASP* 3.4 3.2 + - - -
494E GLY* 1.3 73.2 - - - -
496E LYS* 1.3 75.6 + - + +
498E LEU* 3.0 3.4 + - - +
499E LEU* 3.0 31.0 + - - +
517E SER 3.5 3.8 + - - +
518E VAL* 3.4 7.4 - - - +
519E SER* 2.4 49.2 + - - -
522E ALA* 3.5 18.1 - - + +
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Residues in contact with LYS 496 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495B ASP* 3.7 22.3 + - + +
499B LEU* 3.4 25.2 - - + +
519B SER* 4.1 2.1 + - - +
521B GLY* 4.0 19.5 - - - -
522B ALA* 3.5 27.1 - - - +
525B LEU* 3.7 9.9 - - + -
549B GLU* 4.7 11.2 + - - +
550B SER 6.1 0.6 - - - +
470E ASP* 2.9 34.1 + - + +
494E GLY 3.5 0.2 - - - -
495E ASP* 1.3 83.3 - - + +
497E ALA* 1.3 61.7 + - - +
498E LEU 3.2 0.5 + - - -
499E LEU 3.7 0.2 + - - -
500E ALA* 3.1 25.8 + - - +
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Residues in contact with ALA 497 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B LEU* 4.0 9.6 - - - -
470E ASP* 3.5 38.2 + - + +
473E MET* 3.5 22.2 - - + -
474E HIS* 3.9 13.5 - - + +
477E LEU* 4.0 4.0 - - - +
495E ASP 3.3 0.4 - - - -
496E LYS* 1.3 79.5 - - - +
498E LEU* 1.3 67.0 + - - +
500E ALA* 3.5 2.6 + - - -
501E ASN* 3.2 24.2 + - - +
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Residues in contact with LEU 498 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473E MET* 3.9 7.9 - - + -
477E LEU* 4.9 2.9 - - + +
494E GLY 3.4 15.5 + - - +
495E ASP 3.0 4.3 + - - +
497E ALA* 1.3 85.8 - - - +
499E LEU* 1.3 67.2 + - + +
500E ALA 3.1 0.3 + - - -
501E ASN 3.2 10.2 + - - +
502E ALA* 3.2 11.3 + - - -
505E LEU* 3.9 18.9 - - + +
511E LEU* 3.1 35.9 - - + -
513E MET* 4.5 5.4 - - - -
518E VAL* 3.8 30.7 - - + -
522E ALA* 4.8 12.3 - - + +
523E CYS* 5.3 2.5 - - - +
526E LEU* 4.2 22.8 - - + +
556E VAL* 5.8 0.7 - - + -
558E ILE* 4.0 11.7 - - + -
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Residues in contact with LEU 499 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496B LYS* 3.6 45.3 - - + +
499B LEU* 3.6 12.7 - - + +
500B ALA* 3.7 29.1 - - + +
495E ASP 3.0 19.7 + - - +
496E LYS 4.5 1.1 - - - +
498E LEU* 1.3 81.8 - - + +
500E ALA* 1.3 61.8 + - - +
501E ASN 3.0 1.0 + - - -
502E ALA* 3.3 16.1 + - - +
522E ALA* 3.9 20.2 - - + +
525E LEU* 4.5 4.7 - - + -
526E LEU* 3.9 44.4 - - + +
529E LYS* 6.0 0.2 - - + -
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Residues in contact with ALA 500 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499B LEU* 3.8 22.7 - - + -
525B LEU* 3.9 17.9 - - + -
529B LYS* 2.9 46.3 + - + +
474E HIS* 4.8 1.6 - - - +
496E LYS 3.1 19.0 + - - +
497E ALA 4.1 0.2 - - - +
498E LEU 3.0 1.8 - - - -
499E LEU* 1.3 77.3 - - - +
501E ASN* 1.3 69.3 + - - +
502E ALA 3.5 0.4 - - - -
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Residues in contact with ASN 501 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529B LYS* 4.1 8.4 - - - +
474E HIS* 3.0 29.3 + - - -
477E LEU* 3.7 29.2 + - + +
478E SER* 3.5 31.5 - - - +
497E ALA 3.2 18.3 - - - +
498E LEU 3.2 4.7 + - - +
499E LEU 3.0 0.2 - - - -
500E ALA* 1.3 88.0 + - - +
502E ALA* 1.3 64.8 + - - +
503E SER* 3.3 2.5 - - - -
504E LYS* 3.4 19.0 + - + +
505E LEU* 3.8 8.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il